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It's a dark and stormy night in Gotham City... Harley Quinn enters into an antique shop and douses the store owner with Joker Gas. The Joker enters and steals a green dragon statue.

Later, the police investigate the crime scene and wonder why Joker would only take one jade statue, worth maybe a hundred thousand dollars - especially when rumor has it that he's hurting for funds. Batman examines a fragment of the statue that had been left behind and takes it for further study.

Back in the Batcave he discovers that the "jade" is emitting low-level radiation, meaning it's actually Kryptonite. According to Alfred, the "Laughing Dragon" has gained a bad reputation for being cursed, since all of its owners died prematurely. Now realizing what the Joker is up to, Batman heads off to Metropolis.

Out over Metropolis, terrorists seize control of Air Force One, with the President of the United States on board. Lois Lane is among the press corps on board, virtually guaranteeing Superman's prompt arrival. He easily defeats the terrorists and saves the passengers. When he returns to the ground, Lois tries to let him know how she feels, but they are interrupted when robbers attack the First National Bank, and Superman must fly.

Lex Luthor sourly reads about the President thanking "Metropolis's Favorite Son" and heads down to his car. However, the car speeds blindly through traffic, and the driver is revealed to be not Mercy, but Harley Quinn. Joker enters the car and explains that he is broke due to Batman's success in closing down his operations in Gotham City. So he offers Luthor a deal: for one billion dollars, he'll kill Superman. Luthor is initially skeptical, but changes his mind when Joker shows him the Kryptonite statue. He accepts the offer.

Bruce Wayne is visiting Metropolis to work on a deal with Luthor. Lois is immediately taken with him, and Bruce returns her interest. Much to Clark Kent's displeasure, Lois accepts Bruce's invitation to dinner.

That night, Joker sets up his base in Metropolis, gassing a local crime boss and taking his hideout and his cowered thugs for his own. The boss is later found, hysterical with laughter, by the Metropolis police.

The next day, an insect-like probe droid, the Wayne/Lex T-7, crawls through a canyon even scaling walls. Bruce is pleased at how well WayneTech and LexCorp's collaboration has worked out in developing the robots for space exploration, but Luthor says the robots would be even more useful for military purposes. But Bruce, who under their agreement has sole control over the technology's uses, firmly squelches the idea.

That night, Batman appears in a Metropolis nightclub, finding a runaway thug from the gang Joker recruited. While Batman is interrogating the thug, Superman arrives, saying he doesn't want Batman's brand of vigilantism in his town. To his astonishment, Batman throws him across the room with a judo move. Superman pushes him against the wall, and the thug escapes. Using his x-ray vision, Superman looks beneath the mask and sees that Batman is Bruce Wayne. Batman then pulls out the fragment of Kryptonite and warns Superman of Joker's plan.

Superman returns to his apartment. His jealousy increases when he gets a call from Lois, who says she's taking the morning off to have breakfast with Bruce. As they talk, he sees a small homing device planted on his cape. Looking out his window, he sees that Batman has followed him to "Clark Kent"'s apartment, and now discovered his secret identity as well.

Things are not going well between Batman and Superman. Lois and Bruce flirt with each other at the Daily Planet, much to Clark's chagrin. But out of her earshot they talk about Joker's location, and Clark drops a warning about Bruce's relationship with Lois.

Over dinner at a rooftop restaurant, Bruce and Lois are getting closer, but Joker arrives and kidnaps Lois, and his thugs send Bruce falling off the roof's edge, though he manages to save himself.

Joker contacts Superman, inviting him to come alone to one of LexCorp's laboratories. In his jealousy, Superman ignores Bruce's warning to "expect the unexpected" from Joker.

While waiting for Superman, Joker breaks the statue in half, saving one half for later just in case.

Superman arrives at the laboratory wearing his Anti-Kryptonite suit. Joker appears confused when the Kryptonite has no effect on him, and Superman quickly gets him to lead him to where Lois is. But just as Superman is about to save Lois, Joker uses his acid flower to destroy the suit. Exposed to the radiation, Superman falls, and Joker starts to electrocute him with his buzzer. Before he can kill Superman, however, Harley Quinn calls and warns that Batman has arrived. Joker leaves, and as soon as Batman enters the room, the doors are sealed and Joker Gas is vented in.

Batman examines the room's contents: barrels of hydrochloric acid, too weak to eat through the walls or door, but instead Batman uses it to dissolve the Kryptonite. Recovering from its effects, Superman is just able to smash their way out of the room, taking Batman and Lois with him. They confront Joker, who distracts them with grenades made to look like marbles. The trio flees the laboratory, which is destroyed in an explosion.

That morning, Lex makes a public statement that the explosion was only a minor problem but is furious with Joker for destroying his property. Clark, among the reporters, hears Luthor mention of his deal with Joker. Luthor confronts Joker and gives him a second chance to kill Superman but insists that it's his last (while the two men are discussing the situation, Harley and Mercy are doing their best to kill each other bare-fisted).

In his apartment, Luthor is rudely awakened by Batman, who has learned about his connection to Joker from Clark. Luthor refuses to tell him anything, but realizes that Batman is a serious enough threat that he must be taken care of as well.

Lois tells Clark that she's planning a transfer to the Planet's Gotham City bureau, feeling that she and Bruce are serious enough that they're practically engaged.

Joker makes his new move and fakes a distress signal from a cruise ship to lure Superman away. As soon as Superman arrives, the distress becomes real when a bomb is detonated on the hull, causing the ship to sink. Batman arrives to check out the situation, and is attacked by a larger, armed version of the Wayne/Lex T-7.

Out at sea, Superman repairs the damage to the cruise ship and prevents it sinking. At the same time, Batman flees the Wayne/Lex T-7 using a specially designed jet pack. However, the robot pursues him to the Daily Planet building, where Lois happens to be putting in a late night.

With her in danger of being caught in the crossfire, Batman snatches her up and together they try to run. The pair are cornered by the robot in the printer room. As it tries to push him into the press, his cape and cowl are caught and pulled off, revealing his identity to Lois. Lois manages to distract the robot from killing Bruce, long enough for Superman to arrive and destroy it.

Luthor is informed of the Wayne/Lex T-7's failure and realizes that he'll be connected to the crime. He decides to cut his losses and orders one more meeting with Joker.

Back at her apartment, Lois treats a wound on Bruce's shoulder. She is fuming because Bruce deceived her about his secret identity, and also because she honestly cares for him enough that she can't release the story of the century: "Batman Unmasked!" Superman arrives and asks Bruce for a partnership so that they can take in both their enemies. Batman agrees and the duo leaves.

Meanwhile, Joker and Luthor meet at a LexCorp aeronautics factory, where Luthor informs Joker and Harley that he intends to kill them and frame them for all the mayhem that's been going on. Joker turns the tables and takes both Luthor and Mercy prisoner. Since he can no longer collect his billion dollars, Joker decides on a "consolation prize": Luthor's gigantic and heavily armed Lexwing airship (having Harley paint it so that it resembles a grinning mouth). Luthor asks how much he'll have to pay for his release, but Joker says he isn't interested in money anymore. Instead, he wants to destroy everything Luthor built, just as Batman destroyed everything that he built.

Batman and Superman arrive but are attacked by giant versions of the Wayne/Lex T-7's before they can stop Joker from taking off. Working together, they destroy most of the robots, but then are faced with one that has Mercy strapped to its side as a shield, preventing them from hitting it. Batman manages to get the robot off the ground and Superman deactivates it without hurting Mercy. Mercy tells the heroes of Joker's plans, which Superman realizes means destroying half of Metropolis. The group is confronted by an even larger, more advanced robot. Superman tells Batman to go after Joker while he takes care of the robot. Unfortunately, this one is equipped with the other half of the Laughing Dragon.

Joker goes on a destructive spree over Metropolis. Batman pursues in the Batwing. Joker damages the plane with missiles, and Batman is forced to eject, but manages to board the plane.

While Batman deals with the wing, Superman is pummeled by the robot until it tries to smash him with a heavy door. The door, which had been lined with lead to block Superman's x-ray vision, protects him from the Kryptonite and he destroys the robot, in the process shattering the last of the Kryptonite to pieces. With that job done, Superman heads off to help.

Batman confronts the Joker, leaving Harley to fly the wing, but she only succeeds in shutting off its engines. Fortunately, Superman arrives just in time to steer the wing away from a collision with a building. In the fight, Joker accidentally drops his entire bag of marble grenades. As the grenades start to explode, the heroes save Luthor and Harley. Joker, left behind, desperately, but unsuccessfully, pulls a parachute onto him. Suddenly, the plane tilts and Joker falls onto his side. Joker sees his grenades rolling towards him, and starts to giggle then he starts laughing, growing louder until he finally roars with maniacal, insane, violent laughter. In the explosion, the wing is destroyed, and it crashes into the ocean.

With the troubles over, Angela Chen reports on the incident: Joker's body has not been found. Luthor is under investigation, but it is unlikely he will be charged with any crime. However, Bruce Wayne, discovering that Luthor has been developing military versions of their robots, terminates his deal with LexCorp. Harley is returned to Arkham.

Sadly for Bruce, Lois says she adores him, but can't get over his secret activities. He tells her goodbye, and he and Clark exchange a good natured farewell before Bruce leaves for Gotham, leaving Metropolis and Lois in Superman's care once again.